Switched to mawk, removed commented parts.

gff_merge_transcripts.sh

@@ -40,13 +40,6 @@ get_scorestrand()
     cut -f6,7 > ${1} || error_exit "get_scorestrand failed"
 }
 
-#merge_reynolds()
-#{
-#    # https://bioinformatics.stackexchange.com/a/2273/292
-#    # $1: bed file to merge
-#    cut -f4-6 ${1} | sed 's/\t/_/g' | sort | uniq | awk -v bed=${1} -F '_' '{ system("grep "$1" bed | bedops --merge - "); print $0; }' | paste -d "\t" - - | sed 's/_/\t/g' | sort-bed -
-#}
-
 merge_bedtools()
 {
     # https://bioinformatics.stackexchange.com/q/2265/292
@@ -54,28 +47,11 @@ merge_bedtools()
     # chromosome, score and strand are always the same
     trap '' PIPE && exec \
     bedtools groupby -g 1,4,6,5 -c 2,3 -o min,max -i "stdin" \
-        | awk -v OFS="\t" '{print $1,$5,$6,$2,$3,$4}' \
+        | mawk -v OFS="\t" '{print $1,$5,$6,$2,$3,$4}' \
         | sort-bed - \
         || error_exit "merge_bedtools failed"
 }
 
-#to_gff()
-#{
-#    trap '' PIPE && exec \
-#    awk -v OFS="\t" -v progname=${PROGNAME%.*} '{print $1,progname,"transcript",$2+1,$3,$6,$5,".","gene_id "$4"; transcript_id "$4";"}' - \
-#        || error_exit "to_gff failed"
-#}
-
-#merge_to_gff()
-#{
-#    #trap '' PIPE && exec \
-#    cat - \
-#        | merge_bedtools \
-#        | to_gff \
-#        || error_exit "merge_to_gff failed"
-#}
-
-
 setup()
 {
     workdir=$(mktemp -d)